Interdisciplinary scientific knowledge is necessary but not sufficient when it comes to addressing sustainable transformations, as science increasingly has to deal with normative and value-related issues. A systems perspective on coupled human-environmental systems (HES) helps to address the inherent complexities. Additionally, a thorough interaction between science and society (i.e., transdisciplinarity = TD) is necessary, as sustainable transitions are sometimes contested and can cause conflicts. In order to navigate complexities regarding the delicate interaction of scientific research with societal decisions these processes must proceed in a structured and functional way. We thus propose HES-based TD processes to provide a basis for reorganizing science in coming decades.